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- PDB-3bve: Structural basis for the iron uptake mechanism of Helicobacter py... -

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Basic information

Entry
Database: PDB / ID: 3bve
TitleStructural basis for the iron uptake mechanism of Helicobacter pylori ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE / iron storage / Metal-binding
Function / homology
Function and homology information


bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / identical protein binding / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bacterial non-heme ferritin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, K.H. / Cho, K.J. / Lee, J.H. / Shin, H.J. / Yang, I.S.
CitationJournal: To be Published
Title: Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin
Authors: Kim, K.H. / Cho, K.J. / Lee, J.H. / Shin, H.J. / Yang, I.S.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0219
Polymers125,7456
Non-polymers2763
Water14,592810
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,08436
Polymers502,97924
Non-polymers1,10512
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area93600 Å2
ΔGint-503 kcal/mol
Surface area142340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.709, 128.709, 165.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11F-1009-

HOH

21F-1131-

HOH

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Components

#1: Protein
Ferritin


Mass: 20957.465 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZLI1, ferroxidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 10% isopropanol, 200mM sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 124001 / Num. obs: 119289 / % possible obs: 96.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.5 / % possible all: 86.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.216 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 5988 5 %RANDOM
Rwork0.186 ---
obs0.188 119285 96.24 %-
all-123945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8482 0 18 810 9310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218884
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.92612031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.251085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28726.021485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.475151615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.483156
X-RAY DIFFRACTIONr_chiral_restr0.0760.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026820
X-RAY DIFFRACTIONr_nbd_refined0.1910.24419
X-RAY DIFFRACTIONr_nbtor_refined0.2940.26193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2739
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2177
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.265
X-RAY DIFFRACTIONr_mcbond_it0.5831.55434
X-RAY DIFFRACTIONr_mcangle_it0.94928493
X-RAY DIFFRACTIONr_scbond_it2.16733914
X-RAY DIFFRACTIONr_scangle_it2.3984.53512
X-RAY DIFFRACTIONr_rigid_bond_restr2.27939348
X-RAY DIFFRACTIONr_sphericity_free2.4273811
X-RAY DIFFRACTIONr_sphericity_bonded1.38238655
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 407 -
Rwork0.285 7521 -
all-7928 -
obs--87.11 %

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